NickAkhmetov/CAT-775 - EPIC builders boilerplate, migrate API client (#…

…91)

VERSION.txt

@@ -1 +1 @@
-0.2.5
+0.2.6

setup.cfg

@@ -20,13 +20,14 @@ package_dir =
 packages = find:
 python_requires = >=3.7
 install_requires =
-    vitessce>=3.2.6
-    hubmap-commons>=2.0.12
+    vitessce>=3.2.8
+    hubmap-commons>=2.0.15
     requests>=2.27.1
     nbformat==5.1.3
     zarr>=2.17.2
     aiohttp>=3.8.1
     fsspec>=2022.1.0
+    python-datauri>=2.2.0
 
 [options.packages.find]
 where = src

src/portal_visualization/builder_factory.py

@@ -1,29 +1,23 @@
 from .builders.base_builders import NullViewConfBuilder
 from .builders.sprm_builders import (
-    StitchedCytokitSPRMViewConfBuilder, TiledSPRMViewConfBuilder,
-    MultiImageSPRMAnndataViewConfBuilder
+    StitchedCytokitSPRMViewConfBuilder,
+    TiledSPRMViewConfBuilder,
+    MultiImageSPRMAnndataViewConfBuilder,
 )
 from .builders.imaging_builders import (
     SeqFISHViewConfBuilder,
     IMSViewConfBuilder,
     ImagePyramidViewConfBuilder,
-    NanoDESIViewConfBuilder
+    NanoDESIViewConfBuilder,
 )
 from .builders.anndata_builders import (
     MultiomicAnndataZarrViewConfBuilder,
     SpatialRNASeqAnnDataZarrViewConfBuilder,
     RNASeqAnnDataZarrViewConfBuilder,
-    SpatialMultiomicAnnDataZarrViewConfBuilder
-)
-from .builders.scatterplot_builders import (
-    RNASeqViewConfBuilder, ATACSeqViewConfBuilder
-)
-from .assays import (
-    SEQFISH,
-    MALDI_IMS,
-    NANODESI,
-    SALMON_RNASSEQ_SLIDE
+    SpatialMultiomicAnnDataZarrViewConfBuilder,
 )
+from .builders.scatterplot_builders import RNASeqViewConfBuilder, ATACSeqViewConfBuilder
+from .assays import SEQFISH, MALDI_IMS, NANODESI, SALMON_RNASSEQ_SLIDE
 
 
 # This function processes the hints and returns a tuple of booleans
@@ -40,7 +34,17 @@ def process_hints(hints):
     is_spatial = "spatial" in hints
     is_support = "is_support" in hints
 
-    return is_image, is_rna, is_atac, is_sprm, is_codex, is_anndata, is_json, is_spatial, is_support
+    return (
+        is_image,
+        is_rna,
+        is_atac,
+        is_sprm,
+        is_codex,
+        is_anndata,
+        is_json,
+        is_spatial,
+        is_support,
+    )
 
 
 # This function is the main entrypoint for the builder factory.
@@ -50,18 +54,27 @@ def process_hints(hints):
 # `get_assaytype` is a function which takes an entity UUID and returns
 # a dict containing the assaytype and vitessce-hints for that entity.
 def get_view_config_builder(entity, get_assaytype, parent=None):
-    if (entity.get('uuid') is None):
+    if entity.get("uuid") is None:
         raise ValueError("Provided entity does not have a uuid")
     assay = get_assaytype(entity)
-    assay_name = assay.get('assaytype')
-    hints = assay.get('vitessce-hints', [])
-    is_image, is_rna, is_atac, is_sprm, is_codex, is_anndata, is_json, is_spatial, is_support = process_hints(
-        hints)
+    assay_name = assay.get("assaytype")
+    hints = assay.get("vitessce-hints", [])
+    (
+        is_image,
+        is_rna,
+        is_atac,
+        is_sprm,
+        is_codex,
+        is_anndata,
+        is_json,
+        is_spatial,
+        is_support,
+    ) = process_hints(hints)
 
     # vis-lifted image pyramids
-    if (parent is not None):
-        if (is_support and is_image):
-            ancestor_assaytype = get_assaytype(parent).get('assaytype')
+    if parent is not None:
+        if is_support and is_image:
+            ancestor_assaytype = get_assaytype(parent).get("assaytype")
             if SEQFISH == ancestor_assaytype:
                 # e.g. parent  = c6a254b2dc2ed46b002500ade163a7cc
                 # e.g. support = 9db61adfc017670a196ea9b3ca1852a0

src/portal_visualization/builders/epic_builders.py

@@ -0,0 +1,59 @@
+from abc import ABC, abstractmethod
+from vitessce import VitessceConfig
+from .base_builders import ConfCells
+from ..utils import get_conf_cells
+
+
+# EPIC builders take in a vitessce conf output by a previous builder and modify it
+# accordingly to add the EPIC-specific configuration.
+class EPICConfBuilder(ABC):
+    def __init__(self, base_conf: ConfCells, epic_uuid) -> None:
+
+        conf, cells = base_conf
+
+        if conf is None:
+            raise ValueError("ConfCells object must have a conf attribute")
+
+        self._is_plural = isinstance(conf, list)
+
+        if self._is_plural:
+            self._base_conf = [
+                VitessceConfig.from_dict(conf) for conf in conf
+            ]
+        else:
+            self._base_conf: VitessceConfig = VitessceConfig.from_dict(base_conf.conf)
+
+        self._epic_uuid = epic_uuid
+        pass
+
+    def get_conf_cells(self):
+        self.apply()
+        if (self._is_plural):
+            return get_conf_cells([conf.to_dict() for conf in self._base_conf])
+        return get_conf_cells(self._base_conf)
+
+    def apply(self):
+        if self._is_plural:
+            for conf in self._base_conf:
+                self._apply(conf)
+        else:
+            self._apply(self._base_conf)
+
+    @abstractmethod
+    def _apply(self, conf):  # pragma: no cover
+        pass
+
+
+class SegmentationMaskBuilder(EPICConfBuilder):
+
+    def _apply(self, conf):
+        datasets = conf.get_datasets()
+        print(f"Found {len(datasets)} datasets")
+        # Proof of concept using one of the kaggle segmentation masks for now
+        # segmentations = ObsSegmentationsOmeTiffWrapper(
+        #     img_url='https://assets.hubmapconsortium.org/c9d9ab5c9ee9642b60dd351024968627/ometiff-pyramids/VAN0042-RK-3-18-registered-PAS-to-postAF-registered.ome_mask.ome.tif?token=AgndN7NVbn83wwDXjpnY1Y0lDoJj2j7zOGmn1WN6qr9pqdkjKmt9C1XYm4KrlWrOXE9rVJvpnEKrPjIXrlKd1hmDGjV',
+        #     # offsets_path=f'./{name}/{name}/offsets/{name}.segmentations.offsets.json',
+        #     obs_types_from_channel_names=True,
+        # )
+        # dataset.add_object(segmentations)
+        pass

src/portal_visualization/builders/imaging_builders.py

@@ -76,6 +76,7 @@ def get_conf_cells(self, **kwargs):
             )
             if 'separate/' not in path  # Exclude separate/* in MALDI-IMS
         ]
+        found_images = sorted(found_images)
         if len(found_images) == 0:
             message = f"Image pyramid assay with uuid {self._uuid} has no matching files"
             raise FileNotFoundError(message)